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- PDB-3pvi: D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOW... -

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Basic information

Entry
Database: PDB / ID: 3pvi
TitleD34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOWS THAT ASP34 IS DIRECTLY INVOLVED IN DNA RECOGNITION AND INDIRECTLY INVOLVED IN CATALYSIS
Components
  • DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')
  • PROTEIN (PVUII ENDONUCLEASE)
KeywordsHYDROLASE/DNA / COMPLEX (RESTRICTION ENDONUCLEASE-DNA) / MUTANT / PROTEIN/DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding
Similarity search - Function
PVUII Endonuclease, subunit A / Restriction endonuclease, type II, PvuII / Restriction endonuclease, type II, PvuII superfamily / Restriction endonuclease PvuII / PvuII Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme PvuII
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.59 Å
AuthorsHorton, J.R. / Cheng, X.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis.
Authors: Horton, J.R. / Nastri, H.G. / Riggs, P.D. / Cheng, X.
#1: Journal: Embo J. / Year: 1994
Title: Structure of PvuII Endonuclease with Cognate DNA
Authors: Cheng, X. / Balendiran, K. / Schildkraut, I. / Anderson, J.E.
#2: Journal: Proteins / Year: 1994
Title: Expression, Purification, and Crystallization of Restriction Endonuclease PvuII with DNA Containing its Recognition Site
Authors: Balendiran, K. / Bonventre, J. / Knott, R. / Jack, W. / Benner, J. / Schildkraut, I. / Anderson, J.E.
History
DepositionOct 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')
D: DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')
A: PROTEIN (PVUII ENDONUCLEASE)
B: PROTEIN (PVUII ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)44,5614
Polymers44,5614
Non-polymers00
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.800, 86.300, 48.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3') / COGNATE OLIGONUCLEOTIDE


Mass: 3967.585 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (PVUII ENDONUCLEASE)


Mass: 18312.957 Da / Num. of mol.: 2 / Mutation: D34G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Plasmid: PBBE3 / Production host: Escherichia coli (E. coli) / Strain (production host): PR653 / References: UniProt: P23657
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 52 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.5 mg/mlprotein1drop
21.6 mg/mlDNA duplex1drop
38 %(v/v)PEG40001drop
40.3 mMEDTA1drop
5200 mMsodium acetate1drop
68 %(v/v)PEG40001reservoir
70.3 mMEDTA1reservoir
8200 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.14
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14 Å / Relative weight: 1
ReflectionResolution: 1.59→40 Å / Num. obs: 52374 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.75 % / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.59→1.66 Å / Rsym value: 0.317 / % possible all: 69
Reflection
*PLUS
Num. measured all: 301390

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1PVI

1pvi


Resolution: 1.59→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 5047 10 %RANDOM
Rwork0.205 ---
obs0.205 50527 98.5 %-
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 1.59→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 526 0 269 3471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.59→1.66 Å / Total num. of bins used: 8 /
Rfactor% reflection
Rfree0.345 10 %
Rwork0.317 -
obs-69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARRAM11.DNATOPH11.DNA
X-RAY DIFFRACTION3DNA-RNA-MULTI-ENDO.PARAMMULTI_TOP_NDBX3.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.345 / % reflection Rfree: 10 % / Rfactor Rwork: 0.317

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